Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168146.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_388, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29457
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:4973 original size:68 final size:68
Alignment explanation
Indices: 4864--4998 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 68
4854 AAATTGAACA
* *
4864 TTTAATACCAATGTTCGAATACATGGAGTTAATGAACGCGACCAACCTTCAATCTGCCAACAATC
1 TTTAATACCAATATTCGAATACATGGAGGTAATGAACGCGACCAACCTTCAATCTGCCAACAATC
4929 TCT
66 TCT
* * * * * * *
4932 TTTAATACCGATATTCGAGTATATGGAGGTGATGGATGCGACCAACCTTCAATCTGCCAATAATC
1 TTTAATACCAATATTCGAATACATGGAGGTAATGAACGCGACCAACCTTCAATCTGCCAACAATC
4997 TC
66 TC
4999 CAACCCTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (68 bp):
TTTAATACCAATATTCGAATACATGGAGGTAATGAACGCGACCAACCTTCAATCTGCCAACAATC
TCT
Found at i:5046 original size:16 final size:17
Alignment explanation
Indices: 5025--5058 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5015 CCATTGGAAC
5025 TCGAACCCGTGA-TTTT
1 TCGAACCCGTGACTTTT
*
5041 TCGAACTCGTGACTTTT
1 TCGAACCCGTGACTTTT
5058 T
1 T
5059 TGCTCTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (17 bp):
TCGAACCCGTGACTTTT
Found at i:6122 original size:29 final size:29
Alignment explanation
Indices: 6080--6141 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
6070 CCAGTAGCTG
*
6080 TCAGGTTCCAACTGGTAGAAGAAAAACTA
1 TCAGGTTCCAACTGGTACAAGAAAAACTA
*
6109 TCAGGTTTCAACTGGTACAAGAAAAACTA
1 TCAGGTTCCAACTGGTACAAGAAAAACTA
6138 TCAG
1 TCAG
6142 CTTGATAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (29 bp):
TCAGGTTCCAACTGGTACAAGAAAAACTA
Found at i:10057 original size:20 final size:20
Alignment explanation
Indices: 10011--10050 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10001 ATCACATATA
* *
10011 ATTTATTAATAATTTTTTAT
1 ATTTTTTAAAAATTTTTTAT
10031 ATTTTTTAAAAATTTTTTAT
1 ATTTTTTAAAAATTTTTTAT
10051 TGTTTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTTAAAAATTTTTTAT
Found at i:11445 original size:16 final size:17
Alignment explanation
Indices: 11424--11458 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11414 GTCATTTCGG
*
11424 TTCGGTT-TAATCGGTT
1 TTCGGTTGTAATCGATT
11440 TTCGGTTGTAATCGATT
1 TTCGGTTGTAATCGATT
11457 TT
1 TT
11459 AAGATCGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (17 bp):
TTCGGTTGTAATCGATT
Found at i:12586 original size:21 final size:21
Alignment explanation
Indices: 12560--12808 Score: 217
Period size: 21 Copynumber: 12.2 Consensus size: 21
12550 AGCAAAGACA
*
12560 GCAGCAGACTACTAGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
*
12581 GCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
*
12602 --A-C-GTCTACTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
* *
12619 GCAGCAGATTACTGGTTTGCT
1 GCAGCAGACTACTGGTTTCCT
*
12640 GCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
* * *
12661 GTAGCAGATTATTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
* * *
12682 GTAGCAGACTGCTAGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
** * * *
12703 ATAGCAGATTGCTGATTT-CT
1 GCAGCAGACTACTGGTTTCCT
* * * *
12723 --TGC-GTCTGCTGGTTTTCT
1 GCAGCAGACTACTGGTTTCCT
*
12741 GCAGCAGATTACTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
*
12762 GCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
*
12783 ACAGCAGACTACTGGTTTCCT
1 GCAGCAGACTACTGGTTTCCT
*
12804 TCAGC
1 GCAGC
12809 GGGTTTTTTC
Statistics
Matches: 184, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
17 22 0.12
18 5 0.03
19 2 0.01
20 5 0.03
21 150 0.82
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (21 bp):
GCAGCAGACTACTGGTTTCCT
Found at i:12667 original size:42 final size:42
Alignment explanation
Indices: 12560--12808 Score: 253
Period size: 42 Copynumber: 6.1 Consensus size: 42
12550 AGCAAAGACA
* * * *
12560 GCAGCAGACTACTAGTTTCCTGCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
* * *
12602 --A-C-GTCTACTGGTTTCCTGCAGCAGATTACTGGTTTGCT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
* *
12640 GCAGCAGACTGCTGGTTTCCTGTAGCAGATTATTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
* * ** * *
12682 GTAGCAGACTGCTAGTTTCCTATAGCAGATTGCTGATTT-CT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
* * *
12723 --TGC-GTCTGCTGGTTTTCTGCAGCAGATTACTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
* *
12762 GCAGCAGACTGCTGGTTTCCTACAGCAGACTACTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
*
12804 TCAGC
1 GCAGC
12809 GGGTTTTTTC
Statistics
Matches: 169, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
38 57 0.34
39 5 0.03
40 2 0.01
41 5 0.03
42 100 0.59
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (42 bp):
GCAGCAGACTGCTGGTTTCCTGCAGCAGATTACTGGTTTCCT
Found at i:12779 original size:122 final size:122
Alignment explanation
Indices: 12562--12803 Score: 358
Period size: 122 Copynumber: 2.0 Consensus size: 122
12552 CAAAGACAGC
* *
12562 AGCAGACTACTAGTTTCCTGCAGCAGACTGCTGGTTTCCTACGTCTACTGGTTTCCTGCAGCAGA
1 AGCAGACTACTAGTTTCCTACAGCAGACTGCTGATTTCCTACGTCTACTGGTTTCCTGCAGCAGA
* ** * *
12627 TTACTGGTTTGCTGCAGCAGACTGCTGGTTTCCTGTAGCAGATTATTGGTTTCCTGT
66 TTACTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAGCAGACTACTGGTTTCCTGT
* * * * * * *
12684 AGCAGACTGCTAGTTTCCTATAGCAGATTGCTGATTTCTTGCGTCTGCTGGTTTTCTGCAGCAGA
1 AGCAGACTACTAGTTTCCTACAGCAGACTGCTGATTTCCTACGTCTACTGGTTTCCTGCAGCAGA
12749 TTACTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAGCAGACTACTGGTTTCCT
66 TTACTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAGCAGACTACTGGTTTCCT
12804 TCAGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
122 106 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (122 bp):
AGCAGACTACTAGTTTCCTACAGCAGACTGCTGATTTCCTACGTCTACTGGTTTCCTGCAGCAGA
TTACTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAGCAGACTACTGGTTTCCTGT
Found at i:13616 original size:29 final size:30
Alignment explanation
Indices: 13552--13640 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 30
13542 AATAATTGTG
* * *
13552 TGAATATTACTTTATTATTTTTTTATTATT
1 TGAATATAATTTTATTATTTATTTATTATT
13582 TGAATATAATTTTATT-TTTATTTATTATT
1 TGAATATAATTTTATTATTTATTTATTATT
* * *
13611 TTAATATAATTTAATTATTTATTTTTTATT
1 TGAATATAATTTTATTATTTATTTATTATT
13641 GTTTGGATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 26 0.50
30 26 0.50
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (30 bp):
TGAATATAATTTTATTATTTATTTATTATT
Found at i:19086 original size:18 final size:17
Alignment explanation
Indices: 19063--19097 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19053 GATTTATTCT
19063 TCTTCTCCCTTTCTTTCC
1 TCTTCT-CCTTTCTTTCC
*
19081 TCTTCTCTTTTCTTTCC
1 TCTTCTCCTTTCTTTCC
19098 CTCTCTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTCCTTTCTTTCC
Found at i:19094 original size:17 final size:15
Alignment explanation
Indices: 19072--19105 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
19062 TTCTTCTCCC
19072 TTTCTTTCCTCTTCTCT
1 TTTCTTTCC-C-TCTCT
19089 TTTCTTTCCCTCTCT
1 TTTCTTTCCCTCTCT
19104 TT
1 TT
19106 AGAACAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTCCCTCTCT
Found at i:21612 original size:17 final size:17
Alignment explanation
Indices: 21590--21624 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21580 TGATAATGTA
21590 ATTACCAGA-ATGATCTT
1 ATTACCA-ATATGATCTT
21607 ATTACCAATATGATCTT
1 ATTACCAATATGATCTT
21624 A
1 A
21625 AACTTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
ATTACCAATATGATCTT
Found at i:22294 original size:222 final size:221
Alignment explanation
Indices: 21909--22352 Score: 870
Period size: 222 Copynumber: 2.0 Consensus size: 221
21899 AACTAGGTTT
21909 TTTTTGCCTGTGCTTTGCACGATTAATCTTTTAAAAATAAAAAATAAACTAACTTTAGAAAAATC
1 TTTTTGCCTGTGCTTTGCACGATTAATCTTTTAAAAATAAAAAATAAACTAACTTTAGAAAAATC
*
21974 AAAAAATTAAAATAACAATTGTTTTGAAGAAATAAATTATTATTAAAAAAAATGAAATTGTGAAA
66 AAAAAATTAAAATAACAATTGTTTTGAAGAAATAAATTATTATTAAAAAAAATGAAATCGTGAAA
22039 TCTATAAAAAAATAAAAAGTGAAAAATTAGTAAAATTTATTTATATTTATTATTTTTTAAAGATT
131 TCTATAAAAAAATAAAAAGTGAAAAATTAGTAAAATTTATTTATATTTATTATTTTTTAAAGATT
22104 TATTTTCAAATCATTAATGCATGGAA
196 TATTTTCAAATCATTAATGCATGGAA
22130 TTTTTGCCTGTGCTTTGCACGATTAATCTTTTAAAAATAAAAAATAAACTAACTTTAGAAAAAAT
1 TTTTTGCCTGTGCTTTGCACGATTAATCTTTTAAAAATAAAAAATAAACTAACTTTAG-AAAAAT
22195 CAAAAAATTAAAATAACAATTGTTTTGAAGAAATAAATTATTATTAAAAAAAATGAAATCGTGAA
65 CAAAAAATTAAAATAACAATTGTTTTGAAGAAATAAATTATTATTAAAAAAAATGAAATCGTGAA
22260 ATCTATAAAAAAATAAAAAGTGAAAAATTAGTAAAATTTATTTATATTTATTATTTTTTAAAGAT
130 ATCTATAAAAAAATAAAAAGTGAAAAATTAGTAAAATTTATTTATATTTATTATTTTTTAAAGAT
22325 TTATTTTCAAATCATTAATGCATGGAA
195 TTATTTTCAAATCATTAATGCATGGAA
22352 T
1 T
22353 ATATAAAAAT
Statistics
Matches: 221, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
221 58 0.26
222 163 0.74
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (221 bp):
TTTTTGCCTGTGCTTTGCACGATTAATCTTTTAAAAATAAAAAATAAACTAACTTTAGAAAAATC
AAAAAATTAAAATAACAATTGTTTTGAAGAAATAAATTATTATTAAAAAAAATGAAATCGTGAAA
TCTATAAAAAAATAAAAAGTGAAAAATTAGTAAAATTTATTTATATTTATTATTTTTTAAAGATT
TATTTTCAAATCATTAATGCATGGAA
Found at i:23627 original size:2 final size:2
Alignment explanation
Indices: 23620--23645 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23610 GGAATCTAAT
23620 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23646 GATAAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24471 original size:25 final size:27
Alignment explanation
Indices: 24443--24503 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 27
24433 TATATATAAT
24443 ATAATTTTCTTTTATTTT-GAATTT-A
1 ATAATTTTCTTTTATTTTCGAATTTAA
* ** *
24468 ATAAATTAGTTTTATTTTCTAATTTAA
1 ATAATTTTCTTTTATTTTCGAATTTAA
24495 ATATATTTT
1 ATA-ATTTT
24504 ACATAATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 15 0.56
26 5 0.19
27 4 0.15
28 3 0.11
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
ATAATTTTCTTTTATTTTCGAATTTAA
Found at i:25176 original size:23 final size:23
Alignment explanation
Indices: 25132--25176 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25122 CTTGCTCTTA
*
25132 AAATTTTAATTATTTTATATTAT
1 AAATTTTAATTATTTTAAATTAT
*
25155 AAATTTTTA-TATTTTCAAATTA
1 AAATTTTAATTATTTT-AAATTA
25177 ATATTCAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATTTTAATTATTTTAAATTAT
Found at i:26592 original size:19 final size:18
Alignment explanation
Indices: 26559--26595 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
26549 GGGGCAATTA
*
26559 ATATAGATAATATTAACT
1 ATATAAATAATATTAACT
26577 ATATAAATATATATTAACT
1 ATATAAATA-ATATTAACT
26596 TAAATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATAAATAATATTAACT
Done.